<html><head><meta http-equiv="content-type" content="text/html; charset=utf-8"> <style>
	.KEYW {color: #933;}
	.COMM {color: #bbb; font-style: italic;}
	.NUMB {color: #393;}
	.STRN {color: #393;}
	.REGX {color: #339;}
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	</style></head><body><pre><span class='line'>  1</span> <span class="NAME">Bio.functions.include_once</span><span class="PUNC">(</span><span class="STRN">"Bio::Align"</span><span class="PUNC">)</span><span class="PUNC">;</span><span class="WHIT">
<span class='line'>  2</span> </span><span class="COMM">/**
<span class='line'>  3</span>  * @lends Bio.AlignIO
<span class='line'>  4</span>  */</span><span class="WHIT">
<span class='line'>  5</span> </span><span class="NAME">Bio.AlignIO</span><span class="WHIT"> </span><span class="PUNC">=</span><span class="WHIT"> </span><span class="NAME">Class.create</span><span class="PUNC">(</span><span class="NAME">Bio.Root</span><span class="PUNC">,</span><span class="PUNC">{</span><span class="WHIT"> 
<span class='line'>  6</span>   </span><span class="COMM">/**
<span class='line'>  7</span>    * Bio.AlignIO
<span class='line'>  8</span>    * @author Lee Katz &lt;lskatz@gmail.com>
<span class='line'>  9</span>    * @class Input/output stream for multiple sequence alignments
<span class='line'> 10</span>    * @constructs
<span class='line'> 11</span>    * @extends Bio.Root
<span class='line'> 12</span>    * @todo somehow use $super to get default variables too
<span class='line'> 13</span>    */</span><span class="WHIT">
<span class='line'> 14</span> </span><span class="WHIT">  </span><span class="NAME">initialize</span><span class="PUNC">:</span><span class="WHIT"> </span><span class="KEYW">function</span><span class="PUNC">(</span><span class="NAME">$super</span><span class="PUNC">)</span><span class="WHIT"> </span><span class="PUNC">{</span><span class="WHIT">
<span class='line'> 15</span> </span><span class="WHIT">    </span><span class="NAME">this.options</span><span class="WHIT"> </span><span class="PUNC">=</span><span class="WHIT"> </span><span class="NAME">Object.extend</span><span class="PUNC">(</span><span class="PUNC">{</span><span class="WHIT">
<span class='line'> 16</span> </span><span class="WHIT">      </span><span class="NAME">file</span><span class="PUNC">:</span><span class="KEYW">false</span><span class="PUNC">,</span><span class="WHIT"> </span><span class="COMM">// TODO accept a filename</span><span class="WHIT">
<span class='line'> 17</span> </span><span class="WHIT">      </span><span class="NAME">format</span><span class="PUNC">:</span><span class="KEYW">false</span><span class="PUNC">,</span><span class="WHIT">
<span class='line'> 18</span> </span><span class="WHIT">      </span><span class="NAME">fileText</span><span class="PUNC">:</span><span class="KEYW">false</span><span class="WHIT"> </span><span class="COMM">// the string contents of a file</span><span class="WHIT">
<span class='line'> 19</span> </span><span class="WHIT">    </span><span class="PUNC">}</span><span class="PUNC">,</span><span class="WHIT"> </span><span class="NAME">arguments</span><span class="PUNC">[</span><span class="NUMB">1</span><span class="PUNC">]</span><span class="PUNC">||</span><span class="WHIT"> </span><span class="PUNC">{</span><span class="WHIT"> </span><span class="PUNC">}</span><span class="PUNC">)</span><span class="PUNC">;</span><span class="WHIT">
<span class='line'> 20</span> </span><span class="WHIT">    </span><span class="COMM">// check for required parameters</span><span class="WHIT">
<span class='line'> 21</span> </span><span class="WHIT">    </span><span class="KEYW">if</span><span class="PUNC">(</span><span class="NAME">this.options.fileText</span><span class="PUNC">==</span><span class="KEYW">false</span><span class="PUNC">)</span><span class="PUNC">{</span><span class="WHIT">
<span class='line'> 22</span> </span><span class="WHIT">      </span><span class="NAME">this.throw</span><span class="PUNC">(</span><span class="STRN">"AlignIO requires a fileText parameter"</span><span class="PUNC">)</span><span class="PUNC">;</span><span class="WHIT">
<span class='line'> 23</span> </span><span class="WHIT">    </span><span class="PUNC">}</span><span class="WHIT">
<span class='line'> 24</span> </span><span class="WHIT">    
<span class='line'> 25</span>     </span><span class="COMM">// get the correct AlignIO object</span><span class="WHIT">
<span class='line'> 26</span> </span><span class="WHIT">    </span><span class="KEYW">if</span><span class="PUNC">(</span><span class="PUNC">!</span><span class="NAME">this.options.format</span><span class="PUNC">)</span><span class="PUNC">{</span><span class="WHIT">
<span class='line'> 27</span> </span><span class="WHIT">      </span><span class="NAME">this.options.format</span><span class="PUNC">=</span><span class="NAME">this.guessFormat</span><span class="PUNC">(</span><span class="NAME">this.options.fileText</span><span class="PUNC">)</span><span class="PUNC">;</span><span class="WHIT">
<span class='line'> 28</span> </span><span class="WHIT">    </span><span class="PUNC">}</span><span class="WHIT">
<span class='line'> 29</span> </span><span class="WHIT">    </span><span class="KEYW">var</span><span class="WHIT"> </span><span class="NAME">format</span><span class="PUNC">=</span><span class="NAME">this.options.format</span><span class="PUNC">;</span><span class="WHIT">
<span class='line'> 30</span> </span><span class="WHIT">    </span><span class="KEYW">return</span><span class="WHIT"> </span><span class="KEYW">new</span><span class="WHIT"> </span><span class="NAME">Bio.AlignIO</span><span class="PUNC">[</span><span class="NAME">format</span><span class="PUNC">]</span><span class="PUNC">(</span><span class="NAME">this.options</span><span class="PUNC">)</span><span class="PUNC">;</span><span class="WHIT">
<span class='line'> 31</span> </span><span class="WHIT">  </span><span class="PUNC">}</span><span class="PUNC">,</span><span class="WHIT">
<span class='line'> 32</span> </span><span class="WHIT">  </span><span class="COMM">/** 
<span class='line'> 33</span>    * returns a string representing the format
<span class='line'> 34</span>    * @param str The sequence string
<span class='line'> 35</span>    * @TODO do more than just FASTA
<span class='line'> 36</span>    * @returns String
<span class='line'> 37</span>    */</span><span class="WHIT">
<span class='line'> 38</span> </span><span class="WHIT">  </span><span class="NAME">guessFormat</span><span class="PUNC">:</span><span class="KEYW">function</span><span class="PUNC">(</span><span class="NAME">str</span><span class="PUNC">)</span><span class="PUNC">{</span><span class="WHIT">
<span class='line'> 39</span> </span><span class="WHIT">    </span><span class="KEYW">var</span><span class="WHIT"> </span><span class="NAME">line</span><span class="PUNC">=</span><span class="NAME">str.split</span><span class="PUNC">(</span><span class="STRN">"\n"</span><span class="PUNC">)</span><span class="PUNC">;</span><span class="WHIT">
<span class='line'> 40</span> </span><span class="WHIT">    </span><span class="KEYW">for</span><span class="PUNC">(</span><span class="KEYW">var</span><span class="WHIT"> </span><span class="NAME">i</span><span class="PUNC">=</span><span class="NUMB">0</span><span class="PUNC">;</span><span class="NAME">i</span><span class="PUNC">&lt;</span><span class="NAME">line.length</span><span class="PUNC">;</span><span class="NAME">i</span><span class="PUNC">++</span><span class="PUNC">)</span><span class="PUNC">{</span><span class="WHIT">
<span class='line'> 41</span> </span><span class="WHIT">      </span><span class="KEYW">if</span><span class="PUNC">(</span><span class="NAME">line</span><span class="PUNC">[</span><span class="NAME">i</span><span class="PUNC">]</span><span class="PUNC">.</span><span class="NAME">match</span><span class="PUNC">(</span><span class="REGX">/^>/</span><span class="PUNC">)</span><span class="PUNC">)</span><span class="PUNC">{</span><span class="WHIT">
<span class='line'> 42</span> </span><span class="WHIT">        </span><span class="NAME">i</span><span class="PUNC">++</span><span class="PUNC">;</span><span class="WHIT">
<span class='line'> 43</span> </span><span class="WHIT">        </span><span class="COMM">// if it has something other than ATCG or whitespace then it is not a fasta</span><span class="WHIT">
<span class='line'> 44</span> </span><span class="WHIT">        </span><span class="KEYW">if</span><span class="PUNC">(</span><span class="NAME">line</span><span class="PUNC">[</span><span class="NAME">i</span><span class="PUNC">]</span><span class="PUNC">.</span><span class="NAME">match</span><span class="PUNC">(</span><span class="REGX">/[^ATCG\s]/</span><span class="PUNC">)</span><span class="PUNC">)</span><span class="PUNC">{</span><span class="WHIT">
<span class='line'> 45</span> </span><span class="WHIT">          </span><span class="NAME">i</span><span class="PUNC">--</span><span class="PUNC">;</span><span class="WHIT">
<span class='line'> 46</span> </span><span class="WHIT">          </span><span class="KEYW">continue</span><span class="PUNC">;</span><span class="WHIT">
<span class='line'> 47</span> </span><span class="WHIT">        </span><span class="PUNC">}</span><span class="WHIT">
<span class='line'> 48</span> </span><span class="WHIT">        </span><span class="KEYW">return</span><span class="WHIT"> </span><span class="STRN">'fasta'</span><span class="PUNC">;</span><span class="WHIT">
<span class='line'> 49</span> </span><span class="WHIT">      </span><span class="PUNC">}</span><span class="WHIT">
<span class='line'> 50</span> </span><span class="WHIT">    </span><span class="PUNC">}</span><span class="WHIT">
<span class='line'> 51</span> </span><span class="WHIT">    </span><span class="NAME">this.throw</span><span class="PUNC">(</span><span class="STRN">"Could not determine the type of sequence file"</span><span class="PUNC">)</span><span class="PUNC">;</span><span class="WHIT">
<span class='line'> 52</span> </span><span class="WHIT">  </span><span class="PUNC">}</span><span class="PUNC">,</span><span class="WHIT">
<span class='line'> 53</span> </span><span class="WHIT">  </span><span class="COMM">/**
<span class='line'> 54</span>    * Gets the next sequence and returns a Bio::Align compatible object
<span class='line'> 55</span>    * @returns Bio.Align
<span class='line'> 56</span>    */</span><span class="WHIT">
<span class='line'> 57</span> </span><span class="WHIT">  </span><span class="NAME">next_aln</span><span class="PUNC">:</span><span class="KEYW">function</span><span class="PUNC">(</span><span class="PUNC">)</span><span class="PUNC">{</span><span class="WHIT">
<span class='line'> 58</span> </span><span class="WHIT">		</span><span class="NAME">this.notImplemented</span><span class="PUNC">(</span><span class="PUNC">)</span><span class="PUNC">;</span><span class="WHIT">
<span class='line'> 59</span> </span><span class="WHIT">	</span><span class="PUNC">}</span><span class="WHIT">
<span class='line'> 60</span> </span><span class="PUNC">}</span><span class="PUNC">)</span><span class="PUNC">;</span><span class="WHIT">
<span class='line'> 61</span> 
<span class='line'> 62</span> </span></pre></body></html>